BN1817 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
WM 9.6812e-06 5.2657e-02
Layer 5 2.2144e-04 3.1621e-03
Layer 4 6.1930e-04 2.9046e-03
Layer 3 6.8820e-04 2.9896e-02
Layer 6 9.1010e-04 9.5371e-03
Layer 2 1.6575e-03 5.0981e-02
Layer 1 8.0949e-01 5.5142e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.4395 0.5767
SLC24A2 Layer 5 2.1543 0.5378
RNPS1 Layer 5 2.0684 0.5245
ATP1B1 Layer 5 1.9766 0.5209
APBB1 Layer 4 2.0820 0.5189
FLOT1 Layer 6 2.0254 0.5162
FKBP8 Layer 4 2.0215 0.5156
TPI1 Layer 4 2.1250 0.5155
RBX1 Layer 5 1.9854 0.5125
RABAC1 Layer 6 1.9678 0.5120
MAPT Layer 6 1.8799 0.5118
AP2M1 Layer 6 2.1484 0.5118
SPOCK1 Layer 4 2.1719 0.5094
MAP1LC3A Layer 4 2.0352 0.5093
WBP2 Layer 5 1.9541 0.5092
NAA38 Layer 4 1.9678 0.5084
NDUFC2 Layer 5 1.9678 0.5082
EEF1G WM 1.9878 0.5067
NDUFB1 Layer 5 2.0039 0.5065
DNAJC6 Layer 5 2.1680 0.5060
SORL1 Layer 5 2.2324 0.5058
COX6B1 Layer 4 2.1016 0.5056
CLASP2 Layer 4 1.9316 0.5042
PRDX2 Layer 5 2.1387 0.5036
ATP5F1D Layer 4 2.0176 0.5034
PCBP1 Layer 4 2.1484 0.5014
ATP5F1B Layer 4 2.1250 0.5011
STMN1 Layer 4 2.0176 0.5002
ITPK1 Layer 4 2.3594 0.5001
PSMC5 Layer 4 1.9902 0.4997
PSMB6 Layer 5 1.9102 0.4980
UQCR10 Layer 5 2.0547 0.4969
PSMA7 Layer 5 1.9902 0.4967
RNASEK Layer 6 1.9902 0.4963
NDUFS7 WM 1.9717 0.4961
COPE WM 1.9697 0.4961
CTSB Layer 4 2.0957 0.4947
SKP1 Layer 6 2.0586 0.4937
PJA2 Layer 5 2.1016 0.4937
ILF3 Layer 4 1.9102 0.4927
USP22 Layer 5 2.3555 0.4924
CTSD WM 1.9604 0.4923
ENO1 Layer 5 2.0078 0.4912
RUFY3 Layer 4 1.9678 0.4910
DYNLRB1 Layer 4 2.1348 0.4908
SOD1 Layer 5 2.1191 0.4907
TPPP WM 2.1094 0.4901
SMIM29 Layer 5 1.8203 0.4900
COX7A2 Layer 4 2.2871 0.4898
HSPE1 WM 1.9365 0.4890

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1817
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1817_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1817/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1817/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1817/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1817/report/PD/BN1817_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1817/report/PD/BN1817_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 07:49:12
  • Number of Processes: 10
  • Spending Time: 0h 4m